Contacts of the strand formed by residues 76 - 80 (chain B) in PDB entry 1ATT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 76 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.1 18.5 + - - -
74B ASN 4.0 1.0 + - - -
75B ASP* 1.3 75.9 - - - +
77B ILE* 1.3 58.9 + - - +
78B PHE 3.9 0.9 - - - +
326B ILE* 3.6 28.7 - - + +
327B GLU 5.1 6.7 - - - +
328B ASP* 3.7 5.8 - - + +
426B ARG 3.4 7.6 - - - +
427B VAL* 3.3 7.8 - - - +
428B ALA 2.8 29.4 + - - +
429B ASN* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.4 41.5 - - + +
67B LEU* 3.5 29.8 - - + -
68B ALA* 3.7 19.1 - - - +
71B LYS* 3.7 12.3 - - + +
75B ASP 4.1 0.2 - - - +
76B ASN* 1.3 73.5 - - - +
78B PHE* 1.3 66.5 + - - +
79B LEU* 4.2 4.0 - - + -
326B ILE* 4.4 1.4 - - - +
328B ASP* 3.2 8.5 - - - +
425B GLY* 2.9 3.6 - - - -
426B ARG* 2.8 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN 3.9 0.6 - - - -
77B ILE* 1.3 74.0 - - - +
79B LEU* 1.3 61.4 + - - +
326B ILE* 3.9 19.7 - - + +
328B ASP* 2.8 35.7 + - + +
330B PHE* 4.5 3.3 - - - -
372B ALA* 3.5 22.6 - - + +
373B PHE 3.0 37.0 - - - -
374B LEU* 3.6 32.3 - - + -
383B ALA* 4.1 5.2 - - + -
411B VAL* 4.1 5.4 - - + -
413B ILE* 4.6 2.5 - - + -
423B PHE* 3.4 40.6 - + + -
424B MET 3.2 27.6 - - - -
425B GLY* 3.8 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA 5.9 0.2 - - - +
63B PHE* 3.6 32.5 - - + -
64B TYR* 3.9 27.6 - - + -
67B LEU* 3.7 21.1 - - + -
77B ILE* 4.2 4.7 - - + -
78B PHE* 1.3 77.3 - - - +
80B SER* 1.3 70.3 + - - +
81B PRO* 3.9 10.3 - - + +
84B ILE* 3.8 13.0 - - + -
330B PHE* 3.7 18.4 - - + -
370B HIS* 4.3 4.3 - - + -
372B ALA* 4.2 9.4 - - - -
423B PHE* 3.7 4.3 - - - +
424B MET* 3.0 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 1.3 76.3 - - - +
81B PRO* 1.3 64.5 - - - +
82B LEU 3.6 0.3 + - - -
83B SER* 3.1 20.4 + - - -
84B ILE* 3.5 1.7 + - - +
220B ILE* 3.8 11.4 - - - +
370B HIS* 3.3 25.4 + - - -
372B ALA* 5.0 0.4 - - - +
385B ALA* 3.5 27.8 - - - -
422B ILE 2.8 18.9 + - - -
423B PHE* 3.7 10.3 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il